Integrative Biology 200B


Syllabus Spring 1999

Brent D. Mishler -- phone: 2-6810;  e-mail: bmishler@socrates.berkeley.e du
David R. Lindberg --  phone: 2-3926;  e-mail:

Graduate Student Instructor:
Dennis P. Wall -- phone: 3-9556;  email:

Class meeting time: Tu-Th, 12:30 - 3:30 pm ; room 4110 VLSB (N.B. lab meets in rm. 3056 where noted
           &nb sp; below).  Additional drop-in lab sessions will be set up for students to do homework and projects.

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Jan. 19: Introduction: Why do we care? (all) / Phylogenetic reconstruction in a nutshell: homology (BDM)
 LAB:  Term project requirements -- tour of systematics collections, library, labs, and resources
Jan. 21: Phylogenetic reconstruction in a nutshell: characters (BDM)
 LAB: Introduction to MacClade (rm. 3056)  (Wall)

Jan. 26: Phylogenetic reconstruction in a nutshell: trees (BDM)
 LAB: Introduction to PAUP  (rm. 2063 & 3056)  (Wall)
Jan. 28: Phylogenetic reconstruction in a nutshell: classification (DRL)
 LAB:  Using MacClade & PAUP together (rm. 3056)  (Wall)

Feb. 2: What can we do with trees once we have them?  Introduction (DRL)
 LAB: discussion of "tree-thinking" (all)
Feb. 4: Trees 1. Comparing cladograms  (DRL)
 LAB: consensus methods (DRL)


Feb. 9: Biogeography I -- basic principles; ecological vs. historical approaches (DRL)
 LAB: discussion of major schools of biogeography (all)
Feb. 11 Biogeography II -- vicariance biogeography (DRL)
 LAB:  biogeographic algorithms  (rm. 3056)  (Wall)  [PROJECT TOPIC DUE]

Feb. 16: Speciation and related issues: species revisited (BDM)
 LAB:  discussion of species concepts (all)
Feb. 18: Reticulation and phylogenetics (BDM)
 LAB:  coalescence theory; applications in population genetics (BDM)

Feb. 23: Coevolution: community ecology, symbioses, trophic interactions (BDM)
 LAB: Brooks parsimony   (BDM)
Feb. 25: Trees 2. Qualitative character evolution within a cladogram (BDM)
 LAB: discuss progress on projects in class


March 2: Comparing two discrete-state characters on a tree (BDM)
 LAB: Maddison's test  (Wall)  (rm. 3056)
March 4: Adaptation (BDM)
 LAB:  advanced MacClade; analysis of molecular evolution (rm. 3056)  (Wall)

March 9: Use of behavioral data  (DRL)
 LAB:  discussion of adaptation (all)
March 11: Heterochrony  (DRL)
 LAB: advanced MacClade  (Wall)  (rm. 3056)

March 16: Trends; modes and rates of character change (BDM)
 LAB: relative rate tests; the molecular clock?  (rm. 3056)   (Wall)
March 18: Phylogenetics and conservation biology  (DRL)


March 22 - 26:  SPRING BREAK

March 30: Trees 3.  Comparing sister clades within a cladogram: the shape of evolution (BDM)
 LAB: generating random trees (Wall)  (MacClade)
April 1: Adaptive radiations (Wall)
 LAB: discussion of application papers (students to bring papers from their groups)


April 6: Trees 4.  Quantitative character evolution within a cladogram (BDM)
 LAB: discuss progress on projects in class
April 8: Independent contrasts (BDM)
 LAB: discussion of application papers (students to bring papers from their groups)

April 13: ANOVA and ANCOVA approaches (BDM)
 LAB:  statistical applications   (Wall)  (rm. 2063 & 3056)
April 15:  Regression approaches (BDM)
 LAB: statistical applications (Wall)  (rm. 3056)


April 20:  Morphometric comparisons  (DRL)
 LAB: Morphometric applications (DRL)  (rm. 3056)
April 22: Trees 5.  Paleontology and phylogenetic systematics (DRL)
 LAB: discussion: the utility of fossil data in phylogenetic reconstruction (all)

April 27: Stratigraphic parsimony (DRL)
 LAB:  discussion of macroevolution paper (all)
April 29: Macroevolution: patterns of diversification and extinction (DRL)
 LAB:  discussion on levels of selection (all)

May 4: Punctuated Equilibrium ? (DRL)
 LAB: discussion on papers testing for PuncEq (all)
May 6: Conclusion and summary: the central role of phylogenetic systematics in comparative biology


May 14-22:    FINALS WEEK -- student minisymposium -- projects due

Requirements & Grading:

(1/3)  Participation.  Do the reading, come to each class and lab, and participate in discussions.  A few homework assignments will also be given.  Systematics Discussion Group:  attendence is requested for this group as well -- it includes other faculty and older students but complements our course well.

(1/3)  Quizzes.  Two equally-weighted, one-hour quizzes will be given, that emphasize problem solving and conceptual understanding.

(1/3)  Project.  This will be a substantive, comparative analysis of data from a group of the student's choice (with approval of the instructors; we encourage the study of thesis or other study groups).    Based on phylogenetic trees (whether self-generated or from the literature), the project should apply all appropriate comparative methods to evaluate several types of comparative questions.  There should also be a rigorous critique of previous comparative literature on the organismal group of choice.  A written report will be turned in during finals week, in the form of a professional journal publication, that is, with an introduction (containing the literature review and critique), materials and methods section, results (using summary figures -- no raw data), and a discussion (being sure to compare results from the different methodologies applied, and to reach some biological conclusions).  We will schedule a minisymposium at the end of the term where students can give a short presentation of their results.